# HG changeset patch # User lldelisle # Date 1666624846 0 # Node ID 8f71aaf6e59d0aef2830d9ebbe8af0c05aba1fe4 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296 diff -r 000000000000 -r 8f71aaf6e59d cooler_balance.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cooler_balance.xml Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,74 @@ + + Copy and balance a cool file. + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **cooler balance** + tool developped by mirnylab + see https://github.com/mirnylab/cooler + and https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance + + command-line:: + + cp $input $output + cooler balance -p \${GALAXY_SLOTS:-1} --mad-max madmax --min-nnz minnnz --min-count mincount --ignore-diags ignorediags --ignore-dist ignoredist --tol tol --max-iters maxiters cistrans -f + --blacklist 'blacklist' + + + + + diff -r 000000000000 -r 8f71aaf6e59d macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,44 @@ + + 0.8.11 + + + htslib + h5py + cooler + + + + + + + + + + + + cooler --version + + + + + + + + + + + + + + + + + + + + + + 10.1093/bioinformatics/btz540 + + + diff -r 000000000000 -r 8f71aaf6e59d test-data/chr19.1M.bins --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr19.1M.bins Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,62 @@ +chr19 0 1000000 +chr19 1000000 2000000 +chr19 2000000 3000000 +chr19 3000000 4000000 +chr19 4000000 5000000 +chr19 5000000 6000000 +chr19 6000000 7000000 +chr19 7000000 8000000 +chr19 8000000 9000000 +chr19 9000000 10000000 +chr19 10000000 11000000 +chr19 11000000 12000000 +chr19 12000000 13000000 +chr19 13000000 14000000 +chr19 14000000 15000000 +chr19 15000000 16000000 +chr19 16000000 17000000 +chr19 17000000 18000000 +chr19 18000000 19000000 +chr19 19000000 20000000 +chr19 20000000 21000000 +chr19 21000000 22000000 +chr19 22000000 23000000 +chr19 23000000 24000000 +chr19 24000000 25000000 +chr19 25000000 26000000 +chr19 26000000 27000000 +chr19 27000000 28000000 +chr19 28000000 29000000 +chr19 29000000 30000000 +chr19 30000000 31000000 +chr19 31000000 32000000 +chr19 32000000 33000000 +chr19 33000000 34000000 +chr19 34000000 35000000 +chr19 35000000 36000000 +chr19 36000000 37000000 +chr19 37000000 38000000 +chr19 38000000 39000000 +chr19 39000000 40000000 +chr19 40000000 41000000 +chr19 41000000 42000000 +chr19 42000000 43000000 +chr19 43000000 44000000 +chr19 44000000 45000000 +chr19 45000000 46000000 +chr19 46000000 47000000 +chr19 47000000 48000000 +chr19 48000000 49000000 +chr19 49000000 50000000 +chr19 50000000 51000000 +chr19 51000000 52000000 +chr19 52000000 53000000 +chr19 53000000 54000000 +chr19 54000000 55000000 +chr19 55000000 56000000 +chr19 56000000 57000000 +chr19 57000000 58000000 +chr19 58000000 59000000 +chr19 59000000 60000000 +chr19 60000000 61000000 +chr19 61000000 61431566 diff -r 000000000000 -r 8f71aaf6e59d test-data/chr19.size --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr19.size Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,1 @@ +chr19 61431566 diff -r 000000000000 -r 8f71aaf6e59d test-data/chrM.40kb.bins --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.40kb.bins Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,1 @@ +chrM 0 16569 diff -r 000000000000 -r 8f71aaf6e59d test-data/chrM.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,333 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT +TTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTG +GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATC +CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA +AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT +GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT +TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATT +ATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCCGC +CCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCA +ACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA +GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAAT +AGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGA +ACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCAC +ACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTT +AACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGC +GGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTA +GATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACT +CCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCC +TAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGC +CACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG +AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTC +AGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAA +GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTG +GCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGC +TTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTC +AAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGA +GGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAA +CCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCA +ACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCT +TACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG +ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATG +AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCT +GCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGA +CCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGT +CTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTAC +CGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTA +AATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC +CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGT +AAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAA +GCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGA +ACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATG +TTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGA +TTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAAC +AAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA +AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTA +CCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCA +GTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcata +atcacttgttccttaaatagggacctgtatgaatggctccacgagggttc +agctgtctcttacttttaaccagtgaaattgacctgcccgtgaagaggcg +ggcataacacagcaagacgagaagaccctatggagctttaatttaTTAAT +GCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT +AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGT +ACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCC +AATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCT +ATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCA +GGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATT +AAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT +ATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT +ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATT +ATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccggt +aatcgcataaaacttaaaactttacagtcagaggttcaattcctcttctt +aacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAAT +CGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATAC +AACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCC +TTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC +ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCG +CTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTC +AACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTC +AATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCG +CACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATC +ATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCT +TATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG +CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTC +GACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATA +CGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTA +TTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGAC +GCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTACT +TCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGCT +ACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA +GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCC +CCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTA +AATAATAGGAGCTTAAACCCCCTTATTTctaggactatgagaatcgaacc +catccctgagaatccaaaattctccgtgccacctatcacaccccatccta +AAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGG +TTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTACT +CTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT +TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCT +AACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTCC +TCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAAC +AATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTC +ATCATTAATAATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCT +TTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGC +CTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA +AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTAT +CCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAAA +ATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCT +ACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCC +TAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACC +CTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAAT +TCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT +TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATC +ATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACCT +ACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAACG +TAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCC +ACACTCATCGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACT +AATAATCTTATAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGC +CCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA +CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAG +CCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCT +AAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAA +AAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAA +TTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGT +CTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCCA +CTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG +AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTC +TAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGT +AACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAAT +CTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAG +TTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAAC +ATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTGC +TATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG +CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCC +TTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCAC +AACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCC +TCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTC +CCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAA +CACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAAC +ACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA +GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGA +ACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTCC +TAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGTA +GACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCAC +CGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGA +AATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACC +GTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT +ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAA +TAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCTA +TTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTAT +CATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCC +TATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACA +TGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAAT +ATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC +TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCC +CCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAaaa +aaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggcc +tccatgactttttcAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTC +AAAGTTAAATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCG +CAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCAC +CTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC +TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATC +TCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCAT +CCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACG +AGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTAC +TGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACAT +ACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTG +ACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA +TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAAC +AGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGAC +CGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGT +TTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGG +GCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGT +AAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACA +CCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT +AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATAT +TAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAA +AATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCA +TTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCT +ATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGAC +TAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATA +ACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCAT +TTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTA +TGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCT +AGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAG +TTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTA +CGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGG +AAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTA +ATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAA +CACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCC +ATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAG +CCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTA +ACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAG +CACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTC +TGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCA +CTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCC +TAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCAC +CATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTAT +TACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACT +TCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCT +CACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATC +ACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTT +TGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAG +TATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAA +AAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGCC +TTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCC +GCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTA +TTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAAC +AACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCC +TAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACC +GAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATTA +TGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATA +TCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGC +TACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCTA +TTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTA +CTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAAA +CCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCACT +GACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAAC +AACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCCC +CCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGCC +AACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCT +ATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGA +ACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGG +CTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACT +AATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACTC +TCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACTA +GCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTT +ATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTAC +TTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACA +CTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAG +ACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGTA +GTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCAT +TCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAA +ACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGA +CTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCT +CGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGA +CTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAAC +ACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCA +CACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTA +TCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTT +AACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTTA +TTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAG +GCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACAC +TACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCA +CCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCC +ATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCAT +GTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCC +AAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACT +GTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTAC +TCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTC +CAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCAT +CAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAA +TCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGA +TTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAG +GCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAA +GGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGC +AGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCAC +TAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA +GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTC +CACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATA +CTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGA +TATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCT +CCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGT +TTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAA +CGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCT +ATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC 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+CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCT +TAAATAAGACATCACGATG diff -r 000000000000 -r 8f71aaf6e59d test-data/chrM.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa.fai Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,1 @@ +chrM 16569 6 50 51 diff -r 000000000000 -r 8f71aaf6e59d test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,1 @@ +chrM hg19 human mitochondrial genome ${__HERE__}/chrM.fa diff -r 000000000000 -r 8f71aaf6e59d test-data/input.cool Binary file test-data/input.cool has changed diff -r 000000000000 -r 8f71aaf6e59d test-data/input.validPairs.tabix Binary file test-data/input.validPairs.tabix has changed diff -r 000000000000 -r 8f71aaf6e59d test-data/input.validPairs.tabix.tbi Binary file test-data/input.validPairs.tabix.tbi has changed diff -r 000000000000 -r 8f71aaf6e59d test-data/input.validPairs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.validPairs.txt Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,20000 @@ +83 0 chr19 23041923 6434 0 chr19 22468767 6238 42 42 +177 0 chr19 7494919 1129 1 chr19 7590087 1161 42 40 +197 0 chr19 46286176 13818 0 chr19 46765336 13943 42 42 +288 0 chr19 36244729 10819 0 chr19 36745142 10979 42 42 +458 0 chr19 32210012 9428 1 chr19 36832116 11004 42 34 +601 0 chr19 3909853 271 1 chr19 3922275 277 42 42 +602 0 chr19 25351870 7147 1 chr19 25376235 7154 42 42 +711 0 chr19 28229621 8128 0 chr19 27983277 8051 42 42 +775 0 chr19 40964930 12289 1 chr19 41036736 12313 42 42 +782 1 chr19 41390888 12410 1 chr19 34916158 10345 42 42 +830 0 chr19 5802570 767 1 chr19 5605692 722 42 42 +871 0 chr19 21406650 5899 1 chr19 21534141 5936 42 42 +949 0 chr19 19843854 5329 1 chr19 19839772 5326 42 42 +1043 1 chr19 27439787 7847 1 chr19 27577107 7901 42 42 +1131 1 chr19 5100343 603 1 chr19 4752092 472 42 42 +1257 1 chr19 38049729 11386 0 chr19 37952044 11358 42 42 +1420 0 chr19 10387209 2112 1 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You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa diff -r 000000000000 -r 8f71aaf6e59d tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+ diff -r 000000000000 -r 8f71aaf6e59d tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,6 @@ + + + value, dbkey, name, path + +
+ diff -r 000000000000 -r 8f71aaf6e59d workflow_cooler.pdf Binary file workflow_cooler.pdf has changed